Vibration Noise in cab with JBL system w/ sub

I just bought a 2012 Taco with the JBL sub system stock. If I am playing the radio even at normal volume it seems that something in the doors or pillar are vibrating causing a horrible noise. I can't stand it and I'm not sure if anyone else is hearing the same. I understand the subs will vibrate some things but the level of vibration is ridiculous when playing at regular volume. Any suggestions on how to lessen it?

 

I found in my 07 double cab that my sub rubs up against the back of the seat and rumbles even at low volumes. i just put a towel between the seat and the sub cover..problem solved for me

 

because it is junk

 

I have the same problem...if you fold the driver side rear seat down and push against the back panel it stops... I just cut a piece of thick foam and put it back there so the seat pushes against it...problem solved...now if i can stop the rattling on the outside